Sandbox Reserved 660: Difference between revisions

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The P. tomentosa 4CL1 protein consists of 536 residues and the overall structure of 4CL1 consists of two distinctive globular domains, the large N-domain and the small C-domain. The N-domain contain 3 <scene name='Sandbox_Reserved_660/Subdomain/1'>subdomains</scene> N1, N2 and N3. N1 and N2 are the structural similarly larger subdomains and the N3 is the smaller one. Each of these two subdomains has a central eight-stranded <scene name='Sandbox_Reserved_660/Betasheet/1'>β-sheets</scene>(6 parallel and 2 anti-parallel β -strands) that is ﬂanked by two <scene name='Sandbox_Reserved_660/Alpha-helix/1'>α-helices </scene>on one side and four α-helices on the other. Subdomain N3 is mainly consisted of β -barrel formed by eight β-strands and an α-helices and 3<sub>10</sub> helices are also found in this subdomain. Center of the C domain of 4CL1 is a 3-stranded mix β-sheet with a combine of 2 α-helices and 2 antiparallel β–sheet on one side of the stranded mix β–sheet and a single α-helices on the other side.

==~~Catalytic center~~

==AMP-binding pocket==

The AMP binding pocket is mainly located within the N-domain. The highly conserved sequence which corresponds to <scene name='Sandbox_Reserved_660/Binding_site/1'>Q328GYGMTEA335</scene> in 4CL provides the majority of the surface of the binding pocket. The side chain phenyl group of Tyr-330 provide the Van Der Waals interaction to the adenine group of the bound AMP on one side of the binding site ring and on the other side, the adenine group is support by the side chain of Gly-306 and main chain of Ala-307. The N atoms of adenine group could also donate hydrogen bond to the carbonyl oxygen of Gly-329. Several hydrogen bonds are formed between the ribose oxygen atoms and the side chains of Arg-432, Lys-434, and Lys-438 and the phosphate group could also form hydrogen bond with side chain of Thr-333 and Gln-443 and main chain NH of Thr-333.

The catalytic site of the 4CL is located on Lys-523 on the C domain and Lys-438 and Gln-443 on the N domain. there is a Ligand Binding–Induced Conformational Changes, and the conformational changes, was observed in 4CL1 structures upon the binding of AMP. A large cleft was observed between the N- and C-domains in apo-4CL1 (unmodified) and the cleft is closed by an 81˚ rotation of the C-domain relative to the N-domain upon the AMP binding. Because no major internal changes are found in either the N- or C-domain, the closure of the inter domain cleft upon the binding of AMP is a rigid-body movement. The Inter domain movement brings different catalytic residues from the C-domains to substrate binding sites to catalyze the respective partial reactions, such as the adenylate-forming partial reaction, and the thioester-forming partial reaction.

Sandbox Reserved 660: Difference between revisions

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 The P. tomentosa 4CL1 protein consists of 536 residues and the overall  structure of 4CL1  consists of two distinctive globular domains, the large N-domain and the small C-domain. The N-domain contain 3 <scene name='Sandbox_Reserved_660/Subdomain/1'>subdomains</scene> N1, N2 and N3. N1 and N2 are the structural similarly larger subdomains and the N3 is the smaller one. Each of these two subdomains has a central eight-stranded <scene name='Sandbox_Reserved_660/Betasheet/1'>β-sheets</scene>(6 parallel and 2 anti-parallel β -strands) that is ﬂanked by two <scene name='Sandbox_Reserved_660/Alpha-helix/1'>α-helices </scene>on one side and four α-helices on the other. Subdomain N3 is mainly consisted of β -barrel formed by eight β-strands and an α-helices and 3<sub>10</sub> helices are also found in this subdomain. Center of the C domain of 4CL1 is a 3-stranded mix β-sheet with a combine of 2 α-helices and 2 antiparallel β–sheet on one side of the stranded mix β–sheet and a single α-helices on the other side.
-==Catalytic center
+==AMP-binding pocket==
+The AMP binding pocket is mainly located within the N-domain. The highly conserved sequence which corresponds to <scene name='Sandbox_Reserved_660/Binding_site/1'>Q328GYGMTEA335</scene> in 4CL provides the majority of the surface of the binding pocket. The side chain phenyl group of Tyr-330 provide the Van Der Waals interaction to the adenine group of the bound AMP on one side of the binding site ring and on the other side, the adenine group is support by the side chain of Gly-306 and main chain of Ala-307. The N atoms of adenine group could also donate hydrogen bond to the carbonyl oxygen of Gly-329. Several hydrogen bonds are formed between the ribose oxygen atoms and the side chains of Arg-432, Lys-434, and Lys-438 and the phosphate group could also form hydrogen bond with side chain of Thr-333 and Gln-443 and main chain NH of Thr-333.
+The catalytic site of the 4CL is located on Lys-523 on the C domain and Lys-438 and Gln-443 on the N domain. there  is a Ligand Binding–Induced Conformational Changes,  and the conformational changes, was observed in 4CL1 structures upon the binding of AMP. A large cleft was observed between the N- and C-domains in apo-4CL1 (unmodified) and the cleft is closed by an 81˚ rotation of the C-domain relative to the N-domain upon the AMP binding. Because no major internal changes are found in either the N- or C-domain, the closure of the inter domain cleft upon the binding of AMP is a rigid-body movement. The Inter domain movement brings different catalytic residues from the C-domains to substrate binding sites to catalyze the respective partial reactions, such as the adenylate-forming partial reaction, and the thioester-forming partial reaction.